RetrogeneDB ID: retro_meug_1998

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold78:56478..57077(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSMEUG00000006573
• Aliases: None
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_meug_1998
AGAATGGCCAACAGGGGACCTGCTTATGGACTGAGCCGAGAGGTACAGCAAAAAATTGAGAAGCAGTACGATGCTGATCT
GGAGCAGATCCTCATTCAGTGGATTACCACACAGTGCCGCAGGGATGTAGGGCGACCCCAGCCTGGGCGAGAAATTTCCA
AAACTGGCTCAAGGATGGCACGGTACTGTGTGAGCTCATCAATGGGCTATACCCTGAAGGCCAGGGCCCAGTAAAGAAAA
TCCAGGCTTCAGGCATGGCCTTCAAACAGATGGAACAGATTTCTCAGTTCCTGCAGGCGGCTGAACGCTATGGCATCAAT
GCCACTGATATCTTCCAAACTGTGGACCTCTGGGAAGGAAAGAATATGGCCTGTGTGCAGCGGACACTGATGAACCTGGG
TGGATCGGCAGTGGCTCGAGGTGATGGCTTCTTCTCTGGAGATCCTAACTGGTTTCCTAAGAAGTCCAAGGAGAATCCCT
GAAACTTCACAGATAACCAACTGCAGGAGGGCAAGAATGTCATTGGGCTGCAAATGGTCACCAACCGTGGGGCATCTCAG
GCAGGCATGACTGGATATGGGATGCCACGCCAGATCCTC

Alignment

ORF - retro_meug_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.52 %
• Parental protein coverage: 98.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RMANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRRDVGRPQPGRE-NFQNWLKDGTVLCELING
          RMANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRRDVGRPQPGRE.NFQNWLKDGTVLCELING
Retrocopy RMANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRRDVGRPQPGRE<NFQNWLKDGTVLCELING

Parental  LYPEGQGPVKKIQASGMAFKQM-QIYQFLQAAERYGINATDIFQTVDLWEGKNMACVQRTLMNLGGLAVA
          LYPEGQGPVKKIQASGMAFKQM.QI.QFLQAAERYGINATDIFQTVDLWEGKNMACVQRTLMNLGG.AVA
Retrocopy LYPEGQGPVKKIQASGMAFKQMEQISQFLQAAERYGINATDIFQTVDLWEGKNMACVQRTLMNLGGSAVA

Parental  RGDGFFSGDPNWFPKKSKENPRNFTDNQLQEGKNVIGLQMGTNRGASHAGMTGYGMPRQIL
          RGDGFFSGDPNWFPKKSKENP.NFTDNQLQEGKNVIGLQM.TNRGAS.AGMTGYGMPRQIL
Retrocopy RGDGFFSGDPNWFPKKSKENP*NFTDNQLQEGKNVIGLQMVTNRGASQAGMTGYGMPRQIL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1998 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1998 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998 , retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,